ongoing microrna data analyses
DESCRIPTION
Ongoing microRNA data analyses. Geuvadis meeting July 2012 Marc Friedländer and Esther Lizano Xavier Estivill lab Programme for Genes and Disease Center for Genomic Regulation (CRG). Basic analyses. QC ( phred scores) c ontrol for contamination l ength profiling - PowerPoint PPT PresentationTRANSCRIPT
Ongoing microRNA data analyses
Geuvadis meeting July 2012Marc Friedländer and Esther Lizano
Xavier Estivill labProgramme for Genes and Disease
Center for Genomic Regulation (CRG)
Basic analyses
pre-processing
mapping (bowtie format)
annotation break-down
improved miRNA strand annotation
miRNA variant sequence annotation
quantification of miRNAs and variants
QC (phred scores)
control for contamination
length profiling
visualization (bedGraph)
summary statistics)(
Advanced analyses
identification of novel miRNAs with miRDeep2
QC (based on PCA)
allele-specific expression
eQTL / correlation with DNA variants
correlation with mRNA expression
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Some summary statisticsMinimum Median Maximum
Total reads ~1,000,000 ~12,000,000 ~50,000,000
quality filtered 0% 0.01% 2.3%
length filtered 0.5% 1.2% 81%
not mapped 1.9% 3.7% 75%
mapped 15.4% 95.1% 97%
annotated 88% 96% 98%
miRNAs 2% 6% 62%
- we detect 1615 out of 1921 known human miRNAs (>84%)
- we profile ~400 miRNAs robustly (detect them in >90% of the samples)
Novel human miRNA candidates identified by miRDeep2
- we identify 257 novel human miRNA candidates
- of these 64% are computationally estimated to be genuine
- we recover 74% of the known human miRNAs in the data
- (incidentally we also recover 23/25 (92%) Epstein Barr virus miRNAs)
- visual inspection reveals some false positives, more filtering required…
Correlations between miRNA and mRNA target expression (CLL consortium data)
miRNA switches and tuners
- switches turn off the expression of their targets- tuners fine-regulate the expression of their targets
- switch target expression should be very low- tuner target expression should be in the physiologically relevant range
Figure from Lai, Current Biology 2005
Expression of mRNA targets and non-targets (CLL consortium data)
AcknowledgementsEstivill labXavier EstivillEulàlia MartíEsther Lizano
Roderic Guigo labPedro FerreraDavid Gonzales
Leiden University Medical CenterHenk Buermans
University of Geneva Medical SchoolTuuli Lappalainen
IMPPCLorena Pantano